Mass spectrometry (MS) is an analytical technique for determining the presence of molecules in a sample. A sample in the mass spectrometer is vaporized and ionized in an ion source and the mass-to-charge ratio of the resulting ions is determined. A time-of-flight mass spectrometer (TOF MS) determines the mass-to-charge ratio of an ion by measuring the amount of time it takes a given ion in the sample to travel from the ion source to a detector with the assistance of electric fields. The time required for an ion to reach the detector is a direct function of its mass and an inverse function of its charge. A sample may contain a single constituent molecule or an almost infinite number of molecules. The presence of a molecule in the sample may be determined by correlating the information contained in the sample mass spectrum with known or theoretical mass spectra for the molecule or by determining the molecule's structure de novo.
Mass spectroscopy is of particular importance in the area of proteome analysis, which includes the measurement of protein expression in a biological sample to characterize biological processes, such as disease or mechanisms of gene expression. Understanding protein expression is crucial to a complete understanding of biological systems. Used in conjunction with gene expression and metabolic studies, protein expression studies are a key tool in understanding biological systems and developing new diagnostics and treatments.
Unlike mRNA, which only acts as a disposable messenger, proteins implement almost all controlled biological functions and, as a result, are integral to such functions as normal cell activity, disease processes, and drug responses. However, protein expression is not reliably predictable. First, protein expression is not predictable from mRNA expression maps because mRNA transcript levels are not strongly correlated with protein levels. Second, proteins are dynamically modified in biological systems by environmental factors in ways which are not predictable from genetic information. Accordingly, knowledge of a biological system's response to a stimulus such as a drug or a condition such as a disease typically requires a comparison of many “normal” with corresponding “abnormal” samples. Thus, proteome analysis requires the determination of the proteins present in a variety of samples.
Presently, the majority of MS processes utilize an electrospray ionization (ESI) ion source as a means for introducing an ionized sample that originates from a high performance liquid chromatograph (HPLC) into a MS apparatus. One of several desirable features of ESI is that fractions from the chromatography column can proceed directly from the HPLC to the ESI ion source. This desirable feature of ESI, however, means that re-sampling a given portion of the sample (e.g. a certain fraction from the column) is generally not possible because it is difficult to stop the flow of effluent from the HPLC and monitor chromatographic resolution. The operator is thus typically constrained to subjecting to MS analysis only that portion of a composition that is currently exiting the ESI nozzle as an ionized spray. Thus, the operator can not stop information acquisition of a sample and ask for additional information acquisition on the previously eluded portion of the sample based upon knowledge of sample characterization obtained during or after an analysis cycle. In such a case, the operator would have to re-inject the HPLC with the composition assuming some remains. However, each injection of a composition into an HPLC can be considered as different samples because of HPLC reproducibility issues such as, for example, difficulties in maintaining the same retention speed.